The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyze 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after but not at the time of Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.

The Middle Bronze Age at Kaman-Kalehöyük represented by stratum IIIc yields material remains (seals and ceramics) contemporary with the international trade system managed by expatriate Assyrian merchants evidenced at the nearby site of Kültepe/Kanesh. It is therefore also referred to as belonging to the “Assyrian Colony Period” (98). The stratum has revealed three burned architectural units, and it has been suggested that the seemingly site-wide conflagration might be connected to a destruction event linked with the emergence of the Old Hittite state (99). The first burned architectural unit includes Rooms 148, 150, 298, 305, and 306. The second includes Room 153 and 208. The two units were excavated between 1994 and 2003. The third unit includes Room 367 and 370 and was excavated in 2004. Omura (100) suggests that the rooms could belong to a public building, and that it might even be a small trade center based on the types of artifacts recovered. Omura (100) has concluded that the evidence from the first complex indicates a battle between 2 groups took place at the site. It is possible that a group died inside the buildings, mostly perishing in the fire, while another group died in the courtyard.

MA2208-09 (FEY12): 940826, S2 (skeleton 2), North, Sector I, Grid XLV-54 (GG), Assyrian IIIc. The sample comes from the same location as MA2206 above. There were 2 additional skeletons (S3 and S4) found here for a total of 4 individuals. They are thought to represent an opposing group fighting the individuals in Room 153. The skeletons fell on top of one other. They were not damaged by the fire.

In this section we provide a compact overview of the skeletal material sampled for sequencing in the present work. For a more comprehensive summary of the main cultural phases of the Caucasus and Anatolia regions from 4000–1500 BCE, see reference (48).

The Iron Age levels at Kaman-Kalehöyük—including the Hellenistic period—can be divided into 4 architectural substrata from IIa (youngest) to IId (oldest). Substratum IIa can be divided into 5 chronological units based on ceramics. From youngest to oldest these are IIa1–2, IIa3–5, IIab–IIc1, IIc2–3, and IId1–3. In unit IIa1–2 (Hellenistic Period) both human and animal skeletons were found in pits. These fall into 3 different burial types: some containing only animal skeletons, others containing only human skeletons, and some with mixed human and animal skeletons.

Pit P1156 in the North Sector XV: a human skeleton was buried in a flexed position. Human and animal bones were apparently deposited together deliberately. Such burial features appear only in stratum IIa1–2 and may be correlated with a population change as well as possibly linked to incoming Galatians like at Gordion.

One of the pits P1056 in sector XV also belongs to the Hellenistic Period.

MA2197 (FEY3): P1056 94 07 11 North, Sector XV, Grid XXXVI-52 (5) Provisional Layer 10, Hellenistic period. A skeleton of a juvenile aged 5–6 years came from P1056 was found alongside a small pig and four half-complete ceramic vessels.

Based on findings, such as pottery and seals, stratum IIIb can be dated to the late part of the 2nd millennium BCE contemporary with the emergence of the Hittite state (1990 excavation reports).

MA2200-01 (FEY6): HS 89-01, 89 08 17, Sector III, Grid XLI-54 (C), Provisional Layer 48 – IIIb – Old Hittite Period. A partial skeleton was found in the west of section C together with an adult skeleton. Only the upper part of the first skeleton (skull, arms) was preserved (Kaman-Kalehöyük Field Notes 1994).

MA2203-04 (FEY8): 535 950810, North, Sector VI, Grid XXXIV-54 (M), Provisional Layer 61, Old Hittite Period. Skeleton HS95-35 belonging to a juvenile was found after removing room R141 on top. This layer is next to room 161, which is contemporary with stratum IIIb.

Context Stratum IIIc (“Assyrian Colony Period” Samples)

The Middle Bronze Age at Kaman-Kalehöyük represented by stratum IIIc yields material remains (seals and ceramics) contemporary with the international trade system managed by expatriate Assyrian merchants evidenced at the nearby site of Kültepe/Kanesh. It is therefore also referred to as belonging to the “Assyrian Colony Period” (98). The stratum has revealed three burned architectural units, and it has been suggested that the seemingly site-wide conflagration might be connected to a destruction event linked with the emergence of the Old Hittite state (99). The first burned architectural unit includes Rooms 148, 150, 298, 305, and 306. The second includes Room 153 and 208. The two units were excavated between 1994 and 2003. The third unit includes Room 367 and 370 and was excavated in 2004. Omura (100) suggests that the rooms could belong to a public building, and that it might even be a small trade center based on the types of artifacts recovered. Omura (100) has concluded that the evidence from the first complex indicates a battle between 2 groups took place at the site. It is possible that a group died inside the buildings, mostly perishing in the fire, while another group died in the courtyard.

MA2205 (FEY9): HS 11-1, 110705, North, Sector VIII, Grid XXX-55 (WW), Provisional Layer 75, Assyrian IIIc. Skeleton HS 11-01 was found in Sector (opening) VIII under a floor between Pit 1913 and Pit 3117 near pit 3117. It is thought to be a child based on its small size.

MA2206 (FEY10): 940826 S1 (Skeleton1), W4-W7 North, Sector I, Grid XLV-54 (GG) Provisional Layer 27, Assyrian IIIc. Room 153 belongs to one of the burnt architectural complexes that were excavated from Sectors 0, I, XXI, and XXII, and it is associated with the other burnt rooms dating to the Assyrian Colony period. Human skeletons were found between the exit of Room 153 and Wall 6 (Kaman-Kalehöyük Field Notes 1994).

MA2208-09 (FEY12): 940826, S2 (skeleton 2), North, Sector I, Grid XLV-54 (GG), Assyrian IIIc. The sample comes from the same location as MA2206 above. There were 2 additional skeletons (S3 and S4) found here for a total of 4 individuals. They are thought to represent an opposing group fighting the individuals in Room 153. The skeletons fell on top of one other. They were not damaged by the fire.

The multi-period archaeological site of Ovaören site is located in the Nevşehir Province, 20 km south of the Kızılırmak River. The site measures ~500 by ~350 m and consists of three areas main: Yassıhöyük (mound), Topakhöyük (mound), and its large terrace settlement (Fig. S2).

The main mound of Yassıhöyük was enclosed by a city wall 1250 m long during the Late Bronze Age (~1650–1150 BCE) and Middle Iron Age (~950–550 BCE). The Middle Iron Age layers represent a center in the region known as Tabal and belong to the Neo-Hittite cultural sphere (101). Later settlement on the mound dates to the Persian, Hellenistic, and Roman periods, but remains of these periods are mostly scanty.

Excavations conducted in 2013 on the terrace settlement beneath Topakhöyük revealed a number of skeletons in trench GT-137 from an Early Bronze Age context. The trench held 5 m of cultural deposit divided into 6 layers. Although no architectural evidence dated to the Middle Bronze Age was detected in the topmost layer (I), some trace of occupation was indicated by thrash pits that had been sunk into the Early Bronze strata from above. Two stone cist graves (M3 and M4) were found below 30 cm of cultural fill of layer I. Both lacked a cover slab, were empty, and probably robbed (102).

Layer II of GT-137 is represented by architectural remains as well as a mixture of Middle Bronze Age and Early Bronze Age pottery.

Layer III of GT-137 is characterized by large ash pits and scattered stones, especially at the eastern end of the trench, probably constituting a dump. An interesting feature in layer III was a planned cesspit 2 m wide by 2.5 m deep with an inner face created by a single line of stones. Finds, such as a tankard, depas amphikypellon, and sherds of wheel-made plates as well as Syrian Bottles date the stratum to the Early Bronze Age III

Layer IV of GT-137 likewise dates to Early Bronze Age IIIa based on architectural remains and finds, such as a bronze toggle pin, wheel-made plates, Syrian Bottles, and depas amphikypellon.

Layer V of GT-137 was the richest in terms of architectural finds and dates to the Early Bronze Age II. In this layer, 2 different structures and a well were uncovered. The well was filled with stones, pottery, and human skeletons (Figs. S2 and S3). In total, skeletons belonging to 22 individuals, including adults, young adults, and children, must belong to the disturbed Early Bronze Age II graves adjacent to the well (103). Pottery and stones found below the skeletons demonstrate that the water well was consciously filled and closed. The fill consists of dumped stones, sherds and skeletons, and the closing stones demonstrate that the water well was consciously filled and cancelled.

Samples from Ovaören-Topakhöyük:

MA2210: G-137, the well of layer V, individual no. 12.MA2212: G-137, the well of layer V, individual no. 2.MA2213: G-137, the well of layer V, individual no. 10.

The Middle Bronze Age at Kaman-Kalehöyük represented by stratum IIIc yields material remains (seals and ceramics) contemporary with the international trade system managed by expatriate Assyrian merchants evidenced at the nearby site of Kültepe/Kanesh. It is therefore also referred to as belonging to the “Assyrian Colony Period” (98). The stratum has revealed three burned architectural units, and it has been suggested that the seemingly site-wide conflagration might be connected to a destruction event linked with the emergence of the Old Hittite state (99). The first burned architectural unit includes Rooms 148, 150, 298, 305, and 306. The second includes Room 153 and 208. The two units were excavated between 1994 and 2003. The third unit includes Room 367 and 370 and was excavated in 2004. Omura (100) suggests that the rooms could belong to a public building, and that it might even be a small trade center based on the types of artifacts recovered. Omura (100) has concluded that the evidence from the first complex indicates a battle between 2 groups took place at the site. It is possible that a group died inside the buildings, mostly perishing in the fire, while another group died in the courtyard.

MA2208-09 (FEY12): 940826, S2 (skeleton 2), North, Sector I, Grid XLV-54 (GG), Assyrian IIIc. The sample comes from the same location as MA2206 above. There were 2 additional skeletons (S3 and S4) found here for a total of 4 individuals. They are thought to represent an opposing group fighting the individuals in Room 153. The skeletons fell on top of one other. They were not damaged by the fire.